Chrome (or Chromium) protocol handling works differently than in Firefox. Firefox basically keeps track of all that itself, which is why you can configure protocol handling (like magnet links) in the Applications part of the Preferences. Chrome, however, relies on xdg-open.
There are a couple things that you need to do before xdg-open will handle magnet ...

Transmission
The default bittorrent client of Ubuntu Desktop, Transmission, has a command line interface (which is not installed by default, the package is transmission-daemon). The daemon can be setup so that it may be interacted with through the terminal and through a web interface.
Transmission is a good bittorrent client because:
It's lightweight ...

The BitTorrent protocol is a peer-to-peer file sharing protocol used for distributing large amounts of data. The big file is broken down into smaller parts and it automatically fetches parts from multiple hosts at once. It also shares the parts you've already downloaded with others, so that everybody shares and benefits.
The technology itself is perfectly ...

deluge
What is Deluge?
Deluge is a full-featured BitTorrent client for Linux, OS X, Unix and Windows. It uses libtorrent in it's backend and features multiple user-interfaces including: GTK+, web and console. It has been designed using the client server model with a daemon process that handles all the bittorrent activity. The Deluge daemon is able to ...

rtorrent
I have written and detailed tutorial also about installation/configuration of rtorrent. Check it out here Tutorial : Using rtorrent on Linux like a pro
rTorrent Pro's
Lightweight
Ultra-fast Downloading Speed
Very Effective Bittorrent traffic encryption
Supported by all the private trackers
Uses libTorrent as backened. libTorrent
very ...

Comparing the speeds of clients I think this is a difficult question to answer and can only be really tested in lab conditions.
I am one of the Deluge devs and we get quite a few people that rave about the transfer speed however the credit should really go to libtorrent(rasterbar) which does all the heavy lifting and is at the core of Deluge plus many ...

For 12.04 and above
In 12.04 and 13.04, deluge does included x-scheme-handler/magnet=deluge.desktop;
in the desktop file. In my case, transmission was still opening magnet links. I had to tell gvfs-open to prefer deluge with:
gvfs-mime --set x-scheme-handler/magnet deluge.desktop

You can use transmission-cli: sudo apt-get install transmission-cli.
This will provide a CLI for torrents. You can show the contents of a torrent file with:
transmission-show my-file.torrent
To show only files use:
transmission-show my-file.torrent | sed -n -e '/FILES/,$p'
For better user add the following line to your ~/.bashrc:
function tsf { ...

Deluge
Deluge is a fully featured, yet lightweight torrent client that is written in Python and utilises libtorrent(rasterbar) C++ library at its core.
Standalone or Thinclient mode (split core/ui) to enable connecting to daemon (deluged) running remotely or in the background.
Multiple user-interfaces, supports access from most platforms:
GTK UI
...

The problem, in your case, is probably not the data rate but the number of connections. Many internet gateways can't handle many connections at the same time.
You can Limit your maximum amount of simultaneous connections in the Transmission preferences like so:
Try to keep these values very low at first. 5/10 is a good starting point. And increase them ...

All anecdotal here, but after trying a lot I ended up preferring qBittorrent. It is another libtorrent(rasterbar) based client and it performs well for me. Coming from Windows I wanted something with many of the capabilities I was used to with uTorrent and the two I found that best met that criteria were qBittorrent and KTorrent, and since I wasn't using ...

The answer is in fact a bug in deluge packaging (or, perhaps deluge is the same & everything else changed around it... depends on your perspective, I guess.) See the forum topic here for the details.
Basically, setting up xdg-open's config via gconf-editor didn't do anything to resolve the issue, since as of Natty the file-open functionality is handled ...

After searching a bit I came across RatioMaster.NET 0.42 that claims to work under Linux with mono 2.6.3 and hardcoded support for torrent clients uTorrent, BitComet, Azureus, ABC, BitLord, BTuga, BitTornado, Burst, BitTyrant, BitSpirit. So this does not include transmission or deluge but some of these do work native under Linux or work with wine.
Did not ...

For a one-time shutdown you can use
shutdown -h 02:00
To schedule it you can use cron. There are some GUIs for it like gnome-schedule.
But to start machine on schedule you have to look at BIOS/UEFI settings.
Update: check the answers about MythTV and Wake on Plan below to schedule startup.

aria2c
A CLI downloader supporting HTTP, FTP, and Torrents.
To download a torrent:
aria2c file.torrent
You can also point it to a remote torrent file http://some web site here.com/file.torrent so you don't need to download the torrent file first.
Also note you can disable file allocation with this flag: --file-allocation=none.
Aria2c also supports ...

qBittorrent
qBittorrent developers claim to be producing a "free" alternative to uTorrent.
One of their features is Sequential downloading (aka "Download in order")
However, this feature is with a health warning:
Attempts to download the selected torrents in sequential order.
Torrent pieces are usually downloaded in an optimal order which
...

To start rtorrent, just press Ctrl+Alt+T on your keyboard to open Terminal. When it opens, run the command(s) below:
rtorrent
To stop Ctrl+D
To quit Ctrl+q
The above commands you do after pressing Enter, in the rtorrent window.
For more information, see Using rtorrent like a pro

Yes, it is posible.
Open transmision ->Click on the torrent you wish to edit -> Afther you click, you have on transmision top bar a button called Properties click on it.
A new windows should appear
On that windows you have a tab called Files click on it
In this tab you should see some checkboxes, if you cannot see the ckeckboxes,resize the windows and make ...